As we have mentioned on our main website, we are searching for a new GARNet Coordinator. Until now, the job has been advertised for internal Cardiff University applications only, but as of today, anyone is eligible to apply. Would you like to work for GARNet? You can find the job advertisement here: Research Associate, GARNet Coordinator.

What does a GARNet Coordinator do?

Lots of things! The GARNet Coordinator is responsible for managing the day-to-day running of the network – you can find a full job specification on the Cardiff website, but practically, the job includes things like:

Organising regular meetings with our Committee, including meeting room bookings, catering and logistics, taking minutes and ensuring actions from the last meeting are completed;

Identifying opportunities for workshops and events that will benefit the plant science community, and then organising those events – recent past examples include the GARNet Conference, Software Carpentry workshops at Liverpool and Warwick, and an iPlant workshop. You’ll need to find sponsorship, book event space and hotel rooms, organise transport and catering, prepare delegate information packs, and so on;

Staying abreast of what’s currently happening in Arabidopsis and basic plant science research, and networking and liaising with members of the plant science community by attending national and international conferences such as ICAR, SEB or UKPSF;

Planning and developing grant applications for resources or projects identified by the plant science community as being of value – we recently secured renewed funding for GARNet itself, and we were heavily involved with putting together the application for iPlant UK.

The GARNet Coordinator needs to be a plant scientist who is well organised, a good writer, communicator and networker. You will, on occasion, need to travel nationally and internationally, and good computer skills are a must – experience with website management, blog platforms and creative publishing software such as Adobe InDesign and Photoshop are ideal.

If you’d like any more information about the GARNet Coordinator vacancy, please feel free to submit informal enquiries to Ruth Bastow.

During 2014, the GARNet team and committee – together with iPlant collaborators in the US – were busy preparing a grant application for an invited BBSRC capital funding call. Our proposal was to work with iPlant to develop a ‘node’ of iPlant here in the UK. Our application was sucessful and the award was announced at the end of January at the AAAS 2015 meeting.

What is iPlant?

Funded by the US National Science Foundation (NSF) the iPlant Collaborative provides free and open access to ‘cyberinfrastructure’, originally just for plant scientists, but now for all the life sciences. Here’s a short video clip to explain more:

Harnessing the power of some of the world’s most powerful supercomputers, iPlant users can access the cloud-based Data Store, which provides very large amounts of space for researchers to store, and quickly transfer and share ‘big data’ files.

iPlant users also have access to the Discovery Environment – a web-based, graphical interface that provides access to an ever-expanding suite of modular, integrated ‘apps’ for data analysis. Apps can be built either by the iPlant team or by more experienced users, and cover a wide range of analysis needs. They are user-friendly and very intuitive, meaning that even researchers with little or no knowledge of command line computer programming can easily run an app, or create a pipeline of apps, to analyse large and complex data files.

Why do we need iPlant UK?

iPlant, which is free for anyone around the world to use, is currently distributed across three locations in the US – the Texas Advanced Computing Center, the University of Arizona and Cold Spring Harbor Laboratory. Though the high performance computing power it utilises is currently sufficient, iPlant was designed to be extendable to spread resources between even greater numbers of ‘nodes’. iPlant UK will be the first – hopefully of many – international iPlant hubs to ensure the future sustainability of the resource on a global scale.

As we noted in our recent Journal of Experimental Botany paper, one of the drawbacks of having iPlant located solely in the US, is that technical user support is only currently available during US office hours. When we hosted our workshop at the University of Warwick in September 2013, iPlant’s US-based support engineers kindly agreed to be woken up if we needed them – and we did! Clearly that’s not an ideal solution going forwards, especially as the number of worldwide users grows and grows.

As well as having access to technical support on the GMT timezone, the project’s collaborators at the Universities of Warwick, Liverpool, Nottingham and at The Genome Analysis Centre (TGAC), aim to convert existing BBSRC-funded software tools for the iPlant environment. This will increase community access to these useful resources, and their uptake, giving the plant science community even greater opportunities for efficient, effective, collaborative research.

How will it work?

iPlant UK will run as an independent, UK-hosted iPlant node that will centralise compute power and data storage to a single site at TGAC.

The team at TGAC, managed by Dr Tim Stitt and Dr Rob Davey, will work together to install and maintain new and existing hardware infrastructure at TGAC, and once that phase is complete, they will start work to establish and launch the iPlant UK node.

Meanwhile, teams at the Universities of Warwick, Nottingham and Liverpool will convert software tools they have created from their existing formats to the iPlant environment.

University of Liverpool: Next generation sequencing workflows (led by Professor Anthony Hall). Working with the wheat community, the team at Liverpool will optimise a wheat genetic tool bench for next generation sequencing, and a pipeline for mapping-by-sequencing.

University of Warwick: Gene expression, networks and promoter motif tools and pipelines (led by Professor Jim Beynon). The Warwick team will port tools from the PRESTA project into the iPlant environment. These tools include those for identifying differential gene expressions, clustering and network inference, and promoter analysis.

This bumper GARNet Research Roundup begins with two sets of papers in related areas. First are three papers that investigate the biology of plasmodesmatata. These include work from the Faulkner lab at the JIC, the Band lab at Nottingham and a broad European collaboration that includes co-authors from Durham, Cambridge and St Andrews. The second[…]

Naresh Loudya from Royal Holloway University of London discusses a recent paper published in the Philosophical Transactions of the Royal Society B entitled ‘Retrograde signalling in a virescent mutant triggers an anterograde delay of chloroplast biogenesis that requires GUN1 and is essential for survival‘. Apologies for the high background noise early in the recording. http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/05/Loudya_200520_edita-19052020-12.25.mp3Podcast:[…]

This edition of GARNet Research Roundup begins with two studies from the John Innes Centre. The first takes a detailed look at meiosis in Arabidopsis arenosa and the second introduces a novel mode of auxin perception. The third paper from the Grierson lab in Bristol uses innovative methods to assess root-soil cohesion through study of[…]

Andre Kuhn works with Lars Ostergaard at the John Innes Centre and discusses a recent Elife paper entitled ‘Direct ETTIN-auxin interaction controls chromatin states in gynoecium development‘. We discuss a new paradigm for auxin perception in the control gene expression. http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/04/200420_Kuhn_edit-20042020-13.57.mp3Podcast: Play in new window | DownloadSubscribe: iTunes | Android | RSS

Bethany Eldridge and Tom Denbigh are co-first authors on a recent paper in Communications Biology entitled ‘Micro-scale interactions between Arabidopsis root hairs and soil particles influence soil erosion‘. We discuss the innovative experimental procedures that they designed to measure the interaction of root hairs with their environment! http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/04/2004254_Eldridge_edit-24042020-11.16.mp3Podcast: Play in new window | DownloadSubscribe: iTunes[…]

GARNet conducted a short survey to assess community-interest in an UK-focused webinar series that will highlights the excellence in UK plant science. Approximately 100 respondants were supportive of the idea so we are kicking off the GARNet-Presents Webinar series on May 5th 2020. This series owes a huge debt of thanks to the widely popular[…]

Chris Morgan who works at the John Innes Centre discusses a recent PNAS paper entitled ‘Derived alleles of two axis proteins affect meiotic traits in autotetraploid Arabidopsis arenosa‘. We discuss the technical challenges of this research as well as the difficulties working from home (or not) with a super-resolution microscope! http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/04/Morgan_200417_edit-17042020-14.59.mp3Podcast: Play in new window[…]

The use of automatic image analysis in the biological sciences has increased significantly in recent years, especially with automated image capture and the rise of phenotyping. This online course will help improve your understanding of image analysis methods, and improve your practical skills and ability to apply the techniques to your images. You will explore[…]

This Easter edition of the GARNet Research Roundup begins with research from Aberystwyth University that has developed a system for studying self-incompatability in self-compatible Arabidopsis. Next is an outstanding community-focussed study led from the John Innes Centre that outlines the development of new resources that better enable discovery-led science to be conducted within hexaploid wheat.[…]

Ludi Wang and Maurice Bosch work at Aberystwyth University and talk to the GARNet Community podcast about a recent paper in JXBot entitled ‘New opportunities and insights into Papaver self-incompatibility by imaging engineered Arabidopsis pollen‘. We discuss the challenges of live imaging Arabidopsis pollen tubes growing in liquid media!! http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/04/Bosch_Wang_200406_edit-07042020-08.56.mp3Podcast: Play in new window |[…]